Nucleic acids analysis

ABSTRACT

The present invention is partly based on the discovery that adverse factors can prevent an effective extraction of nucleic acids from a biological sample and that novel and unexpected agents and steps may be used to mitigate or remove the adverse factors, thereby dramatically improving the quality of the extracted nucleic acids. As such, one aspect of this invention is a novel method for extracting high quality nucleic acids from a biological sample. The high quality extractions obtained by the novel methods described herein are characterized by high yield and high integrity, making the extracted nucleic acids useful for various applications in which high quality nucleic acid extractions are preferred, e.g., a diagnosis, prognosis or therapy evaluation for a medical condition.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a Continuation Application of U.S. application Ser.No. 12/838,413 filed on Jul. 16, 2010, which claims benefit of U.S.provisional applications 61/226,025 and 61/226,106, both filed on Jul.16, 2009, the contents of each of which are incorporated herein byreference in their entireties.

FIELD OF INVENTION

The present invention relates to the general fields of nucleic acidanalysis in human or other animal subjects, particularly the procurementand analysis of high quality nucleic acids from a biological sample, andin particular, from microvesicles.

BACKGROUND

Small microvesicles shed by cells are known as “exosomes” (Thery et al.,2002). Exosomes are reported as having a diameter of approximately30-100 nm and are shed from many different cell types under both normaland pathological conditions (Thery et al., 2002). Exosomes areclassically formed from the inward invagination and pinching off of thelate endosomal membrane. This results in the formation of amultivesicular body (MVB) laden with small lipid bilayer vesicles(−40-100 nm in diameter), each of which contains a sample of the parentcell's cytoplasm (Stoorvogel et al., 2002). Fusion of the MVB with thecell membrane results in the release of these exosomes from the cell,and their delivery into the blood, urine or other bodily fluids.

Another category of cell-derived vesicles are known as “sheddingmicrovesicles” (Cocucci et al., 2009). These microvesicles, formed bydirectly budding off of the cell's plasma membrane, are moreheterogeneous in size than exosomes, and like exosomes, also contain asample of the parent cell's cytoplasm. Exosomes and sheddingmicrovesicles co-isolate using ultracentrifugation and ultrafiltrationisolation techniques and will, therefore, be collectively referred tohere as microvesicles.

Recent studies reveal that nucleic acids within microvesicles have arole as biomarkers. For example, Skog et. al. describes, among otherthings, the use of nucleic acids extracted from microvesicles in GBMpatient serum for medical diagnosis, prognosis and therapy evaluation(Skog et al., 2008). The use of nucleic acids extracted frommicrovesicles is considered to potentially circumvent the need forbiopsies, highlighting the enormous diagnostic potential of microvesiclebiology (Skog et al., 2008).

In research and development, as well as commercial applications ofnucleic acid biomarkers, it is desirable to extract high quality nucleicacids from biological samples in a consistent and reliable manner. Thepresent invention provides compositions of high quality nucleic acidextractions from microvesicles and other biological samples, methods ofmaking such extractions, and methods of using these high quality nucleicacids in various applications.

BRIEF SUMMARY OF THE INVENTION

In one aspect, the invention is a novel nucleic acid extraction from oneor more microvesicles isolated from a eukaryotic biological sample,wherein 18S rRNA and 28S rRNA are detectable in the extraction.Preferably, the quantitative ratio of 18S rRNA to 28S rRNA detectable inthe novel extractions is within the range of approximately 1:1 toapproximately 1:2; and is preferably approximately 1:2. Biologicalsamples from which the novel extraction may be obtained include, amongother things, any bodily fluid, preferably urine, serum or plasma, andpreferably, are from a mammal, particularly a human. For bodily fluidsamples with a protein concentration of less than 10 mg/ml, such asurine, the novel nucleic acid extraction may further comprise a nucleicacid extraction having an RNA Integrity Number (in all cases, asobtained on an Agilent BioAnalyzer or an equivalent thereof) of greaterthan or equal to 5 and/or may further comprise a nucleic acid yield from20 ml of biological sample of greater than or equal to 50 pg/ml.Similarly, for bodily fluid samples with a protein concentration ofgreater than 10 mg/ml, such as serum or plasma, the novel nucleic acidextraction may further comprise an RNA Integrity Number of greater thanor equal to 3 and/or may further comprise a nucleic acid yield from 1 mlof biological sample is greater than or equal to 50 pg/ml.

In another aspect, the invention is a novel profile of nucleic acid fromone or more microvesicles isolated from a eukaryotic biological sample,wherein 18S rRNA and 28S rRNA are detectable in the profile. Preferably,the quantitative ratio of 18S rRNA to 28S rRNA detectable in the novelprofile is within the range of approximately 1:1 to approximately 1:2;and is preferably approximately 1:2. Biological samples from which thenovel profile may be obtained include, among other things, any bodilyfluid, preferably urine, serum or plasma, and preferably, is from amammal, particularly a human. For bodily fluid samples with a proteinconcentration of less than 10 mg/ml, such as urine, the novel profilemay further comprise an RNA Integrity Number of greater than or equal to5 and/or may further comprise a nucleic acid yield from 20 ml ofbiological sample of greater than or equal to 50 pg/ml. Similarly, forbodily fluid samples with a protein concentration of greater than 10mg/ml, such as serum or plasma, the novel profile may further comprisean RNA Integrity Number of greater than or equal to 3 and/or may furthercomprise a nucleic acid yield from 1 ml of biological sample is greaterthan or equal to 50 pg/ml.

In yet another aspect, the invention is a method of evaluating thequality of a nucleic acid extraction from microvesicles isolated from aeukaryotic biological sample, comprising the steps of: (a) extractingRNA from microvesicles; and (b) measuring the quality of the RNA bydetermining the quantity of 18S and 28S rRNA in the extraction.Preferably, the quantitative ratio of 18S rRNA to 28S rRNA determined inthe novel method is within the range of approximately 1:1 toapproximately 1:2; and is preferably approximately 1:2. Biologicalsamples on which the novel method may be performed include, among otherthings, any bodily fluid, preferably urine, serum or plasma, andpreferably, is from a mammal, particularly a human. For bodily fluidsamples with a protein concentration of less than 10 mg/ml, such asurine, the novel method may further result in the extraction of nucleicacid having an RNA Integrity Number of greater than or equal to 5 and/ormay further result in a nucleic acid yield from 20 ml of biologicalsample of greater than or equal to 50 pg/ml. Similarly, for bodily fluidsamples with a protein concentration of greater than 10 mg/ml, such asserum or plasma, the novel method may further result in the extractionof nucleic acid having an RNA Integrity Number of greater than or equalto 3 and/or may further result in a nucleic acid yield from 1 ml ofbiological sample is greater than or equal to 50 pg/ml.

In a further aspect, the invention is a method of obtaining nucleic acidfrom a biological sample, comprising the steps of: (a) obtaining abiological sample; (b) performing an extraction enhancement operation onthe biological sample; and (c) extracting nucleic acid from thebiological sample. The extraction enhancement operation is comprised of:(a) the addition of one or more enhancement agents to the biologicalsample; or (b) the performance of one or more enhancement steps prior tonucleic acid extraction; or (c) a combination of enhancement agents andenhancement steps. The enhancement agents may include: (i) RNaseinhibitor; (ii) protease; (iii) reducing agent; (iv) decoy substrate,such as synthetic RNA; (v) soluble receptor; (vi) small interfering RNA;(vii) RNA binding molecule, such as anti-RNA antibody, chaperoneprotein, or an RNase inhibitory protein; (ix) RNase denaturingsubstance, such as high osmolarity solution or detergent. The extractionenhancement steps may include: (x) washing; (xi) size-separating RNasefrom the sample; (xii) effecting RNase denaturation through a physicalchange, such as by decreasing temperature, or executing a freeze/thawcycle. The novel method may be performed on a biological sampleincluding, among other things, any bodily fluid, preferably urine, serumor plasma, and preferably, is from a mammal, particularly a human. Inone embodiment, a derivative is obtained from the biological sample andsubjected to the extraction enhancement operation before extractingnucleic acid. Preferably, the derivative is a microvesicle fraction fromthe biological sample. In one embodiment, the microvesicle fraction isobtained by a filtration concentration technique, however other knownisolation techniques may be utilized as well. In a further aspect of theinventive method, the derivative may be treated with a ribonuclease,deoxyribonuclease, or a combination thereof, prior to performance of theenhancement extraction operation. In some aspects, the extractionenhancement operation includes the addition of an RNase inhibitor to thebiological sample, or to the derivative, prior to extracting nucleicacid; preferably the RNase inhibitor has a concentration of greater than0.027 AU (1×) for a sample equal to or more than 1 μl; alternatively,greater than or equal to 0.135 AU (5×) for a sample equal to or morethan 1 μl; alternatively, greater than or equal to 0.27 AU (10×) for asample equal to or more than 1 μl; alternatively, greater than or equalto 0.675 AU (25×) for a sample equal to or more than 1 μl; andalternatively, greater than or equal to 1.35 AU (50×) for a sample equalto or more than 1 μl, wherein the 1× protease concentration refers to anenzymatic condition wherein 0.027 AU or more protease is used to treatmicrovesicles isolated from 1 μl or more bodily fluid; the 5× proteaseconcentration refers to an enzymatic condition wherein 0.135 AU or moreprotease is used to treat microvesicles isolated from 1 μl or morebodily fluid; the 10× protease concentration refers to an enzymaticcondition wherein 0.27 AU or more protease is used to treatmicrovesicles isolated from 1 μl or more bodily fluid; the 25× proteaseconcentration refers to an enzymatic condition wherein 0.675 AU or moreprotease is used to treat microvesicles isolated from 1 μl or morebodily fluid; the 50× protease concentration refers to an enzymaticcondition wherein 1.35 AU or more protease is used to treatmicrovesicles isolated from 1 μl or more bodily fluid. Preferably, theRNase inhibitor is a protease.

In a still further aspect, the invention is a novel kit for obtainingnucleic acids from microvesicles, comprising in one or more containers:(a) a nucleic acid extraction enhancement agent; (b) DNase, RNase, orboth; and (c) a lysis buffer. The novel kit may further compriseinstructions for using the kit. In the novel kits of this invention, thenucleic acid extraction enhancing agent may include: (a) RNaseinhibitor; (b) protease; (c) reducing agent; (d) decoy substrate; (e)soluble receptor; (f) small interfering RNA; (g) RNA binding molecule;(h) RNase denaturing substance; or (i) any combination of any of theforegoing agents as a mixture or individually.

In yet another aspect, the invention is a novel method of analyzing RNAfrom microvesicles, comprising the steps of: (a) obtaining a sample ofmicrovesicles; (b) treating the sample with DNase to eliminate all orsubstantially all of any DNA located outside of or on the surface of themicrovesicles in the sample; (c) extracting RNA from the sample; and (d)analyzing the extracted RNA. The novel method may be performed on abiological sample including, among other things, any bodily fluid,preferably urine, serum or plasma, and preferably, is from a mammal,particularly a human.

In a further aspect, the invention is a novel method for diagnosing,monitoring, or treating a subject, comprising the steps of: (a)isolating a microvesicle fraction from a urine sample from a subject;(b) detecting the presence or absence of a biomarker within themicrovesicle fraction; wherein the biomarker is selected from the groupconsisting of (i) a species of nucleic acid, (ii) the level ofexpression of a nucleic acid, (iii) a nucleic acid variant, and (iv) anycombination of any of the foregoing; and wherein the biomarker isassociated with the presence or absence of a disease or other medicalcondition, or the viability of a treatment option. In some aspects, thebiomarker is an mRNA transcript; for instance, the mRNA transcript maybe selected from the group consisting of: NPHS2 (podocin), LGALS1(Galectin-1), HSPG2 (heparin sulfate proteoglycan); CUBN (cubilin), LRP2(megalin), AQP1 (aquaporin 1), CA4 (carbonic anydrase 4), CLCN5(chloride channel protein 5), BDKRB1 (bradykinin B1 receptor), CALCR(calcitonin receptor), SCNN1D (amiloride-sensitive sodium channelsubunit delta), SLC12A3 (thiazide-sensitive sodium-chloridecotransporter), AQP2 (aquaporin 2), ATP6V1B1 (V-ATPase B1 subunit),SLC12A1 (kidney-specific Na—K—Cl symporter via RT-PCR of RiboAmpedmRNA); more preferably, the mRNA transcript is AQP2 (aquaporin 2) orATP6V1B1 (V-ATPase B1 subunit). In further aspects of the novel methods,the biomarker and disease or other medical condition are selected fromthe group consisting of: (a) NPHS2 (podocin) and glomerular disease,such as steroid-resistant nephritic syndrome; (b) CUBN (cubilin) andproteinuria, such as in Imerslund-Grasbeck syndrome; and (c) AQP2(aquaporin 2) and diabetes insipidus.

In yet another aspect, the invention is an isolated polynucleotidemolecule comprising a first nucleotide sequence that is at least 90%identical to a second nucleotide sequence selected from the groupconsisting of SEQ ID NOS: 1-29; an isolated polynucleotide comprising asegment of a nucleotide sequence selected from SEQ ID NOS: 1-29; or anisolated polynucleotide comprising a sequence of at least 13 nucleotidesthat are the same as any 13-nucleotide sequence in any one of SEQ IDNOS: 1-29. In particular, the foregoing polynucleotide molecules may bea deoxyribonucleotide or a ribonucleotide. In other aspects theinvention is a vector comprising any of the foregoing isolated nucleicacid molecules. In still other aspects, the invention is a host cellcomprising any of the foregoing vectors or any of the foregoing isolatednucleic acid molecules.

In a further aspect, the invention is a novel method of assessing thequality of a nucleic acid extraction from a biological sample,comprising: (a) providing a biological sample; (b) obtaining anextraction of nucleic acids from the biological sample; (c) measuringthe amount of a polynucleotide molecule comprising a segment having anucleotide sequence selected from SEQ NOS: 1-29 in the extraction; and(d) comparing the amount of the polynucleotide molecule against astandard to assess the quality of the nucleic acid extraction. The novelmethod may be performed on any biological sample, for example, a bodilyfluid, in particular, urine, serum or plasma, preferably from a mammalsuch as a human. This novel method may be used in conjunction with anyof the foregoing novel nucleic acid extractions or novel extractionmethods. In particular, the standard used to assess the quality of thenucleic acid extraction may be derived by measuring the amount of apolynucleotide molecule comprising a segment having the nucleotidesequence selected from SEQ NOS: 1-29 in nucleic acid extractions frommore than 5 biological samples.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1F are electron microscopy pictures of urinary multivesicularbodies. Multivesicular bodies (MVB) can be identified in various regionsof the nephron and collecting duct (see arrows). Podo—podocyte,PT—proximal tubule, TDL—thin descending limb, TAL—thick ascending limb,CD-PC—collecting duct principal cell, CD-IC—collecting duct intercalatedcell. Scale bar=200 nm for FIGS. 1A-1F; 500 nm for FIG. 1B.

FIG. 2 is an electron microscopy picture of isolated urinarymicrovesicles. Human urinary microvesicles isolated via differentialultracentrifugation and imaged via TEM using phosphotungstic acid as astain. The scale bar=200 nm.

FIG. 3 is a plot depicting RNA profiles generated with a method of 100kDa MWCO filters. An Agilent BioAnalyzer was used to generate the plot.

FIG. 4 is a plot depicting RNA profiles generated with a method ofultracentrifugation. An Agilent BioAnalyzer was used to generate theplot.

FIGS. 5A-5B are a pair of plots depicting RNA profiles generated with athree step pre-processing method of ×300 g spin, ×17,000 g spin, and 0.8μm filtration (FIG. 5A), or with a one step pre-processing method ofonly a 0.8 μm filtration (FIG. 5B), in each case followed byultracentrifugation. An Agilent BioAnalyzer was used to generate theplots.

FIGS. 6A-6B are a pair of plots depicting RNA profiles generated with athree-step pre-processing method of ×300 g spin, ×17,000 g spin, and 0.8μm filtration (FIG. 6A), or with a one step pre-processing method ofonly a 0.8 μm filtration (FIG. 6B), in each case followed by filtrationconcentration. An Agilent BioAnalyzer was used to generate the plots.

FIG. 7 is a flow chart depicting a new method of nucleic acid extractionfrom urine with an extraction enhancement operation.

FIGS. 8A-8B are a pair of plots depicting RNA profiles generated withmethods using 5× versus 10× concentrated proteases. Microvesicles wereisolated via filtration concentrators from 20 ml urine samples. Plot Arepresents the profile obtained with 5× protease. Plot B represents theprofile obtained with 10× protease. A 1× protease concentration refersto an enzymatic condition wherein 0.027 AU or more protease is used totreat microvesicles isolated from 1 μl or more bodily fluid. A 5×protease concentration refers to an enzymatic condition wherein 0.135 AUor more protease is used to treat microvesicles isolated from 1 μl ormore bodily fluid. One mAU is the protease activity that releasesfolin-positive amino acids and peptides corresponding to 1 gmol tyrosineper minute.

FIGS. 9A-9B are a pair of plots depicting RNA profiles generated withmethods using 25× versus 50× concentrated proteases. Microvesicles wereisolated via filtration concentrators from 40 ml urine samples. Plot Arepresents the profile obtained with 25× protease. Plot B represents theprofile obtained with 50× protease. 1× protease refers to 0.027 AU. OnemAU is the protease activity that releases folin-positive amino acidsand peptides corresponding to 1 gmol tyrosine per minute.

FIG. 10 is a plot depicting the RNA profile of melanoma serum, Sample 1.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNaseinhibitor is 1.6 units/ptl microvesicle suspension buffer.

FIG. 11 is a plot depicting the RNA profile of melanoma serum, Sample 2.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNaseinhibitor is 1.6 units/ptl microvesicle suspension buffer.

FIG. 12 is a plot depicting the RNA profile of melanoma serum, Sample 3.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNaseinhibitor is 1.6 units/ptl microvesicle suspension buffer.

FIG. 13 is a plot depicting the RNA profile of melanoma serum, Sample 4.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNase ininhibitor is 1.6 units/ptl microvesicle suspension buffer.

FIG. 14 is a plot depicting the RNA profile of a melanoma serum, Sample5. RNA was extracted from 1 ml serum with a method using a RNaseinhibitor, Superase-In (Ambion, Inc). The final concentration of theRNase inhibitor is 3.2 units/ptl microvesicle suspension buffer.

FIG. 15 is a plot depicting the RNA profile of a melanoma serum, Sample6. RNA was extracted from 1 ml serum with a method using a RNaseinhibitor, Superase-In (Ambion, Inc). The final concentration of theRNase inhibitor is 3.2 units/ptl microvesicle suspension buffer.

FIG. 16 is a plot depicting the RNA profile of normal serum, Sample 7.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNaseinhibitor is 1.6 units/ptl microvesicle suspension buffer.

FIG. 17 is a plot depicting the RNA profile of a normal serum, Sample 8.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNaseinhibitor is 1.6 units/ptl microvesicle suspension buffer.

FIG. 18 is a plot depicting the RNA profile of normal serum, Sample 9.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration is of the RNaseinhibitor 1.6 units/ptl microvesicle suspension buffer.

FIG. 19 is a plot depicting the RNA profile of normal serum, Sample 10.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNaseinhibitor is 1.6 units/ptl microvesicle suspension buffer.

FIG. 20 is a plot depicting the RNA profile of normal serum, Sample 11.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNaseinhibitor is 3.2 units/ptl microvesicle suspension buffer.

FIG. 21 is a plot depicting the RNA profile of normal serum, Sample 12.RNA was extracted from 1 ml serum with a method using a RNase inhibitor,Superase-In (Ambion, Inc). The final concentration of the RNaseinhibitor is 3.2 units/ptl microvesicle suspension buffer.

FIG. 22 is a flow chart depicting a new method of nucleic acidextraction from a biological sample using an extraction enhancementoperation.

FIGS. 23A-23B are a pair of plots depicting RNA profiles generated withmethods with or without DNase treatment. DNA not located inside themicrovesicles was removed by DNase digestion of the microvesicle pelletisolated from urine samples prior to lysis and nucleic acid extraction.FIG. 23A—profile without DNase digestion using RNeasy Micro Kit. FIG.23B—profile with DNase digestion using RNeasy Micro Kit. FIG.23C—profile without DNase digestion using MirVana Kit. FIG. 23D—profilewith DNase digestion using MirVana Kit. Note the changes in small RNApeak height and area indicated by the arrow in. D suggests that thereare some carry-over of DNA into the sample following phenol/chloroformbased extraction

FIGS. 24A-24B are a pair of plots depicting RNA profiles generated withmethods with or without DNase treatment. DNA not located inside themicrovesicles was removed by DNase digestion of the microvesicle pelletisolated from serum samples prior to lysis and nucleic acid extraction.FIG. 24A—profile without DNase digestion. FIG. 24B—profile with DNasedigestion. FIG. 24C—A pseudo gel showing “apoptotic body”-like ladderswhich might co-isolate with serum-derived microvesicles.

FIGS. 25A-25B are a pair of plots depicting RNA profiles generated withmethods with or without RNase treatments. RNA not located inside themicro-vesicles was removed by RNase digestion of the microvesicle pelletisolated from urine samples prior to lysis and nucleic acid extraction.FIG. 25A—profile without RNase digestion. FIG. 25B—profile with RNasedigestion.

FIGS. 26A-26B are a pair of plots depicting RNA profiles generated fromurinary microvesicles and rat kidney tissue. FIG. 26A—profile from ratkidney tissue. FIG. 26B—profile from urinary microvesicles.

FIGS. 27A-27B are a pair of plots depicting RNA profiles generated fromurinary microvesicles and rat kidney tissue using methods that canenrich small RNA extraction. FIG. 27A—profile from rat kidney tissue.FIG. 27B—profile from urinary microvesicles.

FIGS. 28A-28B are a pair of plots depicting RNA profiles generated fromwhole urine exclusive of microvesicles, which are not captured by theisolation technique, with or without DNase treatments. FIG. 28A—nucleicacids isolated from whole urine without DNase treatment. FIG.28B—nucleic acids isolated from whole urine with DNase treatments.

FIGS. 29A-29B are a pair of plots depicting RNA profiles generated fromurinary microvesicles. FIG. 29A—nucleic acids isolated from urinarymicrovesicles without DNase treatment. FIG. 29B—nucleic acids isolatedfrom microvesicles with DNase treatments.

FIGS. 30A-30B are a pair of plots depicting RNA profiles generated fromnucleic acids extracted from the pellet formed during the 300 g spin.FIG. 30A—nucleic acids isolated from 300 g spin pellets without DNasetreatment. FIG. 30B—nucleic acids isolated from 300 g spin pellets withDNase treatment.

FIGS. 31A-31B are a pair of plots depicting RNA profiles generated fromnucleic acids extracted from the pellet formed during the 17,000 g spin.FIG. 31A—nucleic acid profile from 17,000 g spin pellet without DNasetreatment. FIG. 31B—nucleic acid profile from 17,000 g spin pellet withDNase treatment.

FIGS. 32A-32B are a pair of plots depicting RNA profiles generated frommicrovesicles that underwent RNase and DNase digestion on the outsideprior to microvesicle lysis, with or without intra-microvesicular RNasedigestion. FIG. 32A—nucleic acid profile without intra-microvesicularRNase digestion. FIG. 32B—nucleic acid profile with intra-microvesicularRNase digestion.

FIGS. 33A-33B are a pair of plots depicting RNA profiles generated frommicovesicles that underwent RNase and DNase digestion on the outsideprior to microvesicle lysis and intra-microvesicular RNase digestion,without or without intra-microvesicular DNase digestion. FIG.33A—nucleic acid profile without intra-microvesicular DNase digestion.FIG. 33B—nucleic acid profile with intra-microvesicular DNase digestion.On plot B, the peak just after 20 s is reduced compared the matchingpeak in plot A. The reduction suggests that a small amount of DNasedigestible material is present within exosomes.

FIG. 34A represents BioAnalyzer generated ‘Pseudo gel’ profiles of thepositive identification of RiboAmp amplified mRNA transcripts forbeta-actin and GAPDH in urinary microvesicles by RT-PCR; FIG. 34B is anillustration of the nephron and collecting duct highlighting its sixfunctionally distinct regions. 1. Glomerulus; 2. Proximal Tubule; 3.Thin Descending Limb; 4. Medullary Thick Ascending Limb; 5. DistalConvoluted Tubule; 6. Collecting Ducts.

FIG. 35 represents BioAnalyzer generated pseudo gel profiles of theidentification of mRNA transcripts encoding specific genes from regions1 and 2 of the nephron and collecting duct detected by RT-PCR ofRiboAmped mRNA from urinary microvesicles, specifically: 1. Glomerulus:NPHS2—podocin, LGALS1—Galectin-1, HSPG2—heparan sulfate proteoglycan 2.Proximal Tubule: CUBN—cubilin, LRP2—megalin, AQP1—aquaporin 1,CA4—carbonic anhydrase 4, CLCN5—chloride channel protein 5.

FIG. 36 represents BioAnalyzer generated pseudo gel profiles of theidentification of mRNA transcripts encoding specific genes from regions3-6 of the nephron and collecting duct detected by RT-PCR of RiboAmpedmRNA from urinary microvesicles, specifically: 3. Thin Descending Limb:BDKRB1—bradykinin B1 receptor. 4. Medullary Thick Ascending Limb:CALCR—calcitonin receptor, SCNN1D—amiloride-sensitive sodium channelsubunit delta. 5. Distal Convoluted Tubule: SLC12A3—thiazide-sensitivesodium-chloride cotransporter. 6. Collecting Ducts: AQP2—aquaporin 2,ATP6V1B1—vATPase B1 subunit, SLC12A1—Kidney-specific Na—K—Cl symporter.

FIG. 37A is a pair of BioAnalyzer pseudo gels depicting the expressionof the V-ATPase B1 subunit and AQP2 mRNA by RT-PCR in V-ATPase B1 KO(B1−/−) and wild type (B1+/+) mice; FIG. 37B is a pair of chartsdepicting the expression of the V-ATPase B2 subunit in urinarymicrovesicles and kidney cells from V-ATPase B1 KO (B1−/−) and wild type(B1+/+) mice by real-time PCR analysis. “NS”—not statisticallysignificant.

FIGS. 38A-38C are a trio of plots depicting RNA profiles generated fromurinary microvesicles. Urinary microvesicles were not washed or treatedwith any extraction enhancer before the microvesicle membranes werebroken for nucleic acid extraction. Three samples were used in thisgroup of extractions. The profiles are shown in FIGS. 38A, 38B and 38C,respectively.

FIGS. 39A-39C are a trio of plots depicting RNA profiles generated fromurinary microvesicles. Urinary microvesicles were not washed but weretreated with a RNase inhibitor, RNase-In (Promega), before themicrovesicle membranes were broken for nucleic acid extraction. Threesamples were used in this group of extractions. The profiles are shownin FIGS. 39A, 39B and 39C, respectively.

FIGS. 40A-40C are a trio of plots depicting RNA profiles generated fromurinary microvesicles. Urinary microvesicles were washed but were nottreated with any RNase inhibitor before the microvesicle membranes werebroken for nucleic acid extraction. Three samples were used in thisgroup of extractions. The profiles are shown in FIGS. 40A, 40B and 40C,respectively.

FIGS. 41A-41C are a trio of plots depicting RNA profiles generated fromurinary microvesicles. Urinary microvesicles were washed and treatedwith RNase inhibitor before microvesicle membranes were broken fornucleic acid extraction. Three samples were used in this group ofextractions. The profiles are shown in FIGS. 41A, 41B and 41C,respectively.

FIG. 42 is a list of chromosome regions in which there were more than500 transcript hits in a deep sequencing analysis of RNA extracted fromurinary microvesicles (“spikes”). The numbers indicate the start and endpoint of each chromosomal region. For example,“chrl.−1.91625366.91625741” refers to the region on human chromosome 1between nucleotide nos. 91625366 and 91625741. The corresponding SEQ IDNOS are also indicated.

FIG. 43 is a list of primers used for PCR reaction to amply sequences in10 chromosome regions as indicated. For example,“chrl.−1.91625366.91625741” refers to the region on human chromosome 1between nucleotide nos. 91625366 and 91625741. The primer pair used toamplify this region was “tccagctcacgttccctatt 1 L andccaggtggggagtttgact 1R”. Primers run from 5′ to 3′ as they go from leftto right.

FIGS. 44A-44B are a pair of BioAnalyzer pseudo gels depicting the resultof PCR amplification of 10 spike-rich chromosome regions. The numberingof the lanes at the top of each frame corresponds to the numbering ofthe chromosome regions shown in FIG. 43. In FIG. 44A, a nucleic acidextraction from urinary microvesicles was used as a template for thePCR. In FIG. 44B, a nucleic acid extraction from renal tissue was usedas a template for the PCR.

FIGS. 45-73 are plots depicting the spikes in 29 chromosome regions. Theregions are indicated at the top of each plot. For example, the plot inFIG. 46 refers to the region of “chrl.−1.91625366.91625741,” which isthe region on human chromosome 1 between nucleotide nos. 91625366 and91625741.

DETAILED DESCRIPTION

Microvesicles are shed by eukaryotic cells, or budded off of the plasmamembrane, to the exterior of the cell. These membrane vesicles areheterogeneous in size with diameters ranging from about 10 nm to about5000 nm. The small microvesicles (approximately 10 to 1000 nm, and moreoften approximately 10 to 200 nm in diameter) that are released byexocytosis of intracellular multivesicular bodies are referred to in theart as “exosomes.” The compositions, methods and uses described hereinare equally applicable to microvesicles of all sizes; preferably 10 to800 nm; and more preferably 10 to 200 nm.

In some of the literature, the term “exosome” also refers to proteincomplexes containing exoribonucleases which are involved in mRNAdegradation and the processing of small nucleolar RNAs (snoRNAs), smallnuclear RNAs (snRNAs) and ribosomal RNAs (rRNA) (Liu et al., 2006; vanDijk et al., 2007). Such protein complexes do not have membranes and arenot “microvesicles” or “exosomes” as those terms are used here in.

The present invention is partly based on the discovery that adversefactors can prevent an effective extraction of nucleic acids from abiological sample and that novel and unexpected agents and steps may beused to mitigate or remove the adverse factors, thereby dramaticallyimproving the quality of the extracted nucleic acids. As such, oneaspect of this invention are novel methods for extracting high qualitynucleic acids from a biological sample. The high quality extractionsobtained by the novel methods described herein are characterized by highyield and high integrity, making the extracted nucleic acids useful forvarious applications in which high quality nucleic acid extractions arepreferred.

Broadly described, the novel methods include, for example, the steps ofobtaining a biological sample, mitigating or removing the adversefactors that prevent an effective extraction of nucleic acids from abiological sample, and extracting nucleic acids from the biologicalsample followed, optionally, by nucleic acid analysis.

Applicable biological samples include, for example, a cell, a group ofcells, fragments of cells, cell products including for examplemicrovesicles, cell cultures, bodily tissues from a subject, or bodilyfluids. The bodily fluids can be fluids isolated from anywhere in thebody of the subject, preferably a peripheral location, including but notlimited to, for example, blood, plasma, serum, urine, sputum, spinalfluid, pleural fluid, nipple aspirates, lymph fluid, fluid of therespiratory, intestinal, and genitourinary tracts, tear fluid, saliva,breast milk, fluid from the lymphatic system, semen, cerebrospinalfluid, intra-organ system fluid, ascitic fluid, tumor cyst fluid,amniotic fluid and combinations thereof

A biological sample may sometimes come from a subject. The term“subject” is intended to include all animals shown to or expected tohave microvesicles. In particular embodiments, the subject is a mammal,a human or nonhuman primate, a dog, a cat, a horse, a cow, other farmanimals, or a rodent (e.g. mouse, rat, guinea pig, etc.). The term“subject” and “individual” are used interchangeably herein.

A biological sample may optionally be processed to obtain a biologicalsample derivative before, after, or at the same time as, carrying outthe step of mitigating or removing the adverse effects. The biologicalsample derivative may be a cell, cell debris, a membrane vesicle, or amicrovesicle.

A biological sample is sometimes pre-processed before a biologicalsample derivative such as a microvesicle is obtained. In some instances,the pre-processing step is preferred. For example, a urine sample is maybe pre-processed to obtain urinary microvesicles. The pre-processing maybe achieved by techniques known in the art such as low speedcentrifugation and pre-filtration. For example, urine samples mayundergo a first centrifugation step of 300 g to get rid of largeparticles in the samples. Urine samples may undergo a secondcentrifugation step of 17,000 g to get rid of smaller particles in thesamples. After the second centrifugation step, urine samples may furtherundergo a pre-filtration step, e.g., a 0.8 um pre-filtration step.Alternatively, urine samples may be pre-processed by a—pre-filtrationstep without first undergoing the one or more of the centrifugationsteps.

Membrane vesicles, e.g., microvesicles, may be isolated from abiological sample. In some instances, such isolation may be carried outwithout pre-processing the biological sample in some instances. In otherinstances, such isolation may be carried out after the biological sampleis pre-processed. The isolation step may be advantageous for highquality nucleic acid extraction from a biological sample. For example,the isolation may give rise to advantages such as: 1) the opportunity toselectively analyze disease- or tumor-specific nucleic acids, which maybe obtained by isolating disease- or tumor-specific microvesicles apartfrom other microvesicles within the fluid sample; 2) significantlyhigher yield of nucleic acid species with higher integrity as comparedto the yield/integrity obtained by extracting nucleic acids directlyfrom the fluid sample; 3) scalability, e.g. to detect nucleic acidsexpressed at low levels, the sensitivity can be increased by pelletingmore microvesicles from a larger volume of serum; 4) purer nucleic acidsin that protein and lipids, debris from dead cells, and other potentialcontaminants and PCR inhibitors are excluded from the microvesiclepellets before the nucleic acid extraction step; and 5) more choices innucleic acid extraction methods as microvesicle pellets are of muchsmaller volume than that of the starting serum, making it possible toextract nucleic acids from these microvesicle pellets using small volumecolumn filters.

Methods of isolating microvesicles from a biological sample are known inthe art. For example, a method of differential centrifugation isdescribed in a paper by Raposo et al. (Raposo et al., 1996), a paper bySkog et. al. (Skog et al., 2008) and a paper by Nilsson et. al. (Nilssonet al., 2009). Methods of anion exchange and/or gel permeationchromatography are described in U.S. Pat. Nos. 6,899,863 and 6,812,023.Methods of sucrose density gradients or organelle electrophoresis aredescribed in U.S. Pat. No. 7,198,923. A method of magnetic activatedcell sorting (MACS) is described in a paper by Taylor and Gercel-Taylor(Taylor and Gercel-Taylor, 2008). A method of nanomembraneultrafiltration concentration is described in a paper by Cheruvanky etal. (Cheruvanky et al., 2007). Further, microvesicles can be identifiedand isolated from bodily fluid of a subject by a newly developedmicrochip technology that uses a unique microfluidic platform toefficiently and selectively separate tumor-derived microvesicles (Chenet al.). Each of the foregoing references is incorporated by referenceherein for its teaching of these methods.

In one embodiment of the methods described herein, the microvesiclesisolated from a bodily fluid are enriched for those originating from aspecific cell type, for example, lung, pancreas, stomach, intestine,bladder, kidney, ovary, testis, skin, colorectal, breast, prostate,brain, esophagus, liver, placenta, fetus cells. Because themicrovesicles often carry surface molecules such as antigens from theirdonor cells, surface molecules may be used to identify, isolate and/orenrich for microvesicles from a specific donor cell type (Al-Nedawi etal., 2008; Taylor and Gercel-Taylor, 2008). In this way, microvesiclesoriginating from distinct cell populations can be analyzed for theirnucleic acid content. For example, tumor (malignant and non-malignant)microvesicles carry tumor-associated surface antigens and may bedetected, isolated and/or enriched via these specific tumor-associatedsurface antigens. In one example, the surface antigen isepithelial-cell-adhesion-molecule (EpCAM), which is specific tomicrovesicles from carcinomas of lung, colorectal, breast, prostate,head and neck, and hepatic origin, but not of hematological cell origin(Balzar et al., 1999; Went et al., 2004). In another example, thesurface antigen is CD24, which is a glycoprotein specific to urinemicrovesicles (Keller et al., 2007). In yet another example, the surfaceantigen is selected from a group of molecules such as CD70,carcinoembryonic antigen (CEA), EGFR, EGFRvIII and other variants, Fasligand, TRAIL, transferrin receptor, p38.5, p97 and HSP72. Additionally,tumor specific microvesicles may be characterized by the lack of surfacemarkers, such as CD80 and CD86.

The isolation of microvesicles from specific cell types can beaccomplished, for example, by using antibodies, aptamers, aptameranalogs or molecularly imprinted polymers specific for a desired surfaceantigen. In one embodiment, the surface antigen is specific for a cancertype. In another embodiment, the surface antigen is specific for a celltype which is not necessarily cancerous. One example of a method ofmicrovesicle separation based on cell surface antigen is provided inU.S. Pat. No. 7,198,923. As described in, e.g., U.S. Pat. Nos. 5,840,867and 5,582,981, WO/2003/050290 and a publication by Johnson et al.(Johnson et al., 2008), aptamers and their analogs specifically bindsurface molecules and can be used as a separation tool for retrievingcell type-specific microvesicles. Molecularly imprinted polymers alsospecifically recognize surface molecules as described in, e.g., U.S.Pat. Nos. 6,525,154, 7,332,553 and 7,384,589 and a publication by Bossiet al. (Bossi et al., 2007) and are a tool for retrieving and isolatingcell type-specific microvesicles. Each of the foregoing references isincorporated herein for its teaching of these methods.

In instances when the intended biological derivative is a membranevesicle such as a microvesicle, a step of removing nucleic acids thatare not inside the microvesicle is sometimes performed. Methods ofremoving nucleic acids are well known in the art. For example, to removesuch nucleic acids from a sample, an enzyme digestion step may beperformed. Such enzymes may be a type of ribonuclease that catalyzes theenzymatic digestion of ribonucleic acids or a type of deoxyribonucleasethat catalyzes the enzymatic digestion of deoxyribonucleic acids.

In one aspect of this invention, the novel nucleic acid extractionmethods include a step of removing or mitigating adverse factors thatprevent high quality nucleic acid extraction from a biological sample.Such adverse factors are heterogeneous in that different biologicalsamples may contain various species of such adverse factors. In somebiological samples, factors such as excessive extra-microvesicle DNA mayaffect the quality of nucleic acid extractions from such samples andcontaminate DNA extracted from within microvesicle. In other samples,factors such as excessive endogenous RNase may affect the quality ofnucleic acid extractions from such samples. Many agents and methods maybe used to remove these adverse factors. These methods and agents arereferred to collectively as an “extraction enhancement operation.”

In some instances, the extraction enhancement operation may involve theaddition of nucleic acid extraction enhancement agents to the biologicalsample or derivative. To remove adverse factors such as endogenousRNases, such extraction enhancement agents as defined here may include,but are not limited to, a commercially available RNase inhibitor such asSuperase-In (Ambion Inc.), RNaseIN (Promega Corp.), or other agents thatfunction in a similar fashion; a protease; a reducing agent; a decoysubstrate such as a synthetic RNA; a soluble receptor that can bindRNase; a small interfering RNA (siRNA); a RNA binding molecule, such asan anti-RNA antibody, or a chaperone protein; a RNase denaturingsubstance, such as a high osmolarity solution, a detergent, or acombination thereof. These enhancement agents may exert their functionsin various ways, for example, but not limited to, through inhibitingRNase activity (e.g., RNase inhibitors), through a ubiquitousdegradation of proteins (e.g., proteases), or through a chaperoneprotein (e.g., a RNA-binding protein) that binds and protects RNAs. Inall instances, such extraction enhancement agents remove or mitigatesome or all of the adverse factors in the biological sample that wouldotherwise prevent or interfere with the high quality extraction nucleicacids from the biological sample.

In other instances, the extraction enhancement operation may involve theperformance of one or more process steps. Such processes includeextensive or substantially thorough washing of nucleic acid-containingcomponents of the sample, such as microvesicles; size separation ofRNases from the biological sample; denaturation of proteins in thebiological sample by various techniques including, but not limited to,generating a particular pH condition, a temperature condition, (e.g.,the maintenance of a decreasing or lower temperature), freeze/thawcycles, and combinations thereof.

One surprising manifestation of the use of extraction enhancementoperations, as described herein, is the ability to detect in anextraction of nucleic acid from microvesicles the existence ofsignificant quantities of ribosomal RNA (rRNA). No prior studies areknown to have demonstrated the detection of 18S and 28S rRNA inmicrovesicle nucleic acid extractions. On the contrary, prior studiessuggested that no or little rRNA is present in nucleic acid extractsfrom microvesicles (Skog et al., 2008; Taylor and Gercel-Taylor, 2008;Valadi et al., 2007).

In another aspect of this invention, the performance of an extractionenhancement operation will improve the quality of extracted RNA in termsof RNA integrity number (RIN). Designed by Agilent Technologies(http://www.chem.agilent.com/en-us/products/instrurnents/lab-on-a-chip/pages/gp14975.aspx,accessed Jul. 15, 2010), the RNA integrity number (RIN) is the productof a software tool designed to estimate the integrity of total RNAsamples. The software automatically assigns an integrity number to aneukaryote total RNA sample. Using this tool, sample integrity is notdetermined by the ratio of the 18S and 28S ribosomal bands, but by theentire electrophoretic trace of the RNA sample. This includes thepresence or absence of degradation products. The assigned RIN isindependent of sample concentration, instrument, and analyst, and canserve as a standard for RNA integrity.

In yet another aspect of this invention, the performance of anextraction enhancement operation will improve the quantity or yield ofextracted nucleic acid. For example, using an extraction enhancementoperation, as described herein, one may obtain a nucleic acid yield ofgreater than or equal to 50 pg/ml from a 20 ml low protein biologicalsample such as urine. Alternatively, one may obtain a nucleic acid yieldof greater than or equal to 50 pg/ml from 1 ml of a high proteinbiological sample, such as serum or plasma.

Novel high quality nucleic acid extractions obtained by the methodsdescribed herein may display a combination of the detection of 18S and28S rRNA, preferably in a ratio of approximately 1:1 to approximately1:2; and more preferably, approximately 1:2; a RNA integrity number ofgreater than or equal to 5 for a low protein biological sample, orgreater than or equal to 3 for a high protein biological sample; and anucleic acid yield of greater than or equal to 50 pg/ml from a 20 ml lowprotein biological sample or a 1 ml high protein biological sample.

High quality RNA extractions are highly desirable because RNAdegradation can seriously affect downstream assessment of the extractedRNA, such as in gene expression and mRNA analysis, as well as analysisof non-coding RNA such as small RNA and micro RNA. The novel methodsdescribed herein enable one to extract high quality nucleic acids from abiological sample such as microvesicles so that an accurate analysis ofgene expression and mutational level within the exosomes can be carriedout. In one embodiment, for example, when increased concentrations ofprotease (5×, 10×) are used as an extraction enhancing agent, the amountand integrity of RNA isolated from urinary microvesicles is increasedsignificantly.

Another aspect of this invention provides methods of extracting highquality small RNA from a biological sample such as urine. Small RNA,such as miRNA is particularly susceptible to degradation and loss duringthe process of nucleic acid extraction. In the novel methods heredisclosed, a high concentration of protease is used to remove ormitigate adverse factors that prevent high quality extraction of smallRNAs. In one embodiment, a method to extract nucleic acid, particularlysmall RNA, uses 25× and 50× protease as extraction enhancing agent andis able to obtain significantly increased amounts of small RNA. As usedherein, expressions such as 5×, 10×, 25× and 50× mean 5 times, 10 times,etc. the activity level of protease currently used or recommended incommercially available nucleic acid extraction kits such as the QIAampMinElute Virus Spin Kit.

When the adverse factors affecting extraction have been removed ormitigated, nucleic acid molecules can be isolated from a biologicalsample using any number of procedures that are well-known in the art.Persons of skill will select a particular isolation procedure as beingappropriate for the particular biological sample. Examples of methodsfor extraction are provided in the Examples section herein. In someinstances, with some techniques, it may also be possible to analyze thenucleic acid without extraction from the microvesicle.

In one embodiment, the extracted nucleic acids, including DNA and/orRNA, are analyzed directly without an amplification step. Directanalysis may be performed with different methods including, but notlimited to, nanostring technology. NanoString technology enablesidentification and quantification of individual target molecules in abiological sample by attaching a color coded fluorescent reporter toeach target molecule. This approach is similar to the concept ofmeasuring inventory by scanning barcodes. Reporters can be made withhundreds or even thousands of different codes allowing for highlymultiplexed analysis. The technology is

described in a publication by Geiss et al. (Geiss et al., 2008) and isincorporated herein by reference for this teaching.

In another embodiment, it may be beneficial or otherwise desirable toamplify the nucleic acid of the microvesicle prior to analyzing it.Methods of nucleic acid amplification are commonly used and generallyknown in the art, many examples of which are described herein. Ifdesired, the amplification can be performed such that it isquantitative. Quantitative amplification will allow quantitativedetermination of relative amounts of the various nucleic acids, togenerate a profile as described below.

In one embodiment, the extracted nucleic acid is RNA. The RNA is thenpreferably reverse-transcribed into complementary DNA (cDNA) beforefurther amplification. Such reverse transcription may be performed aloneor in combination with an amplification step. One example of a methodcombining reverse transcription and amplification steps is reversetranscription polymerase chain reaction (RT-PCR), which may be furthermodified to be quantitative, e.g., quantitative RT-PCR as described inU.S. Pat. No. 5,639,606, which is incorporated herein by reference forthis teaching.

Nucleic acid amplification methods include, without limitation,polymerase chain reaction (PCR) (U.S. Pat. No. 5,219,727) and itsvariants such as in situ polymerase chain reaction (U.S. Pat. No.5,538,871), quantitative polymerase chain reaction (U.S. Pat. No.5,219,727), nested polymerase chain reaction (U.S. Pat. No. 5,556,773),self-sustained sequence replication and its variants (Guatelli et al.,1990), transcriptional amplification system and its variants (Kwoh etal., 1989), Qb Replicase and its variants (Miele et al., 1983), cold-PCR(Li et al., 2008), or any other nucleic acid amplification methods,followed by the detection of the amplified molecules using techniqueswell known to those of skill in the art. Especially useful are thosedetection schemes designed for the detection of nucleic acid moleculesif such molecules are present in very low numbers. The foregoingreferences are incorporated herein for their teachings of these methods.

The analysis of nucleic acids present in the microvesicles isquantitative and/or qualitative. For quantitative analysis, the amounts(expression levels), either relative or absolute, of specific nucleicacids of interest within the microvesicles are measured with methodsknown in the art (described below). For qualitative analysis, thespecies of specific nucleic acids of interest within the microvesicles,whether wild type or variants, are identified with methods known in theart.

The invention disclosed here also includes as a novel composition ofmatter, a nucleic acid extraction from microvesicles in which 18S and28S rRNA is detectable in the extraction. Such nucleic acid extractionsmay be achieved using the novel nucleic acid extraction method disclosedin this invention. A high quality nucleic acid extraction frommicrovesicles in a biological sample is desirable in many instances. Insome instances, a tissue sample is not easily accessible. For example abrain tumor sample can not usually be obtained without brain surgery.Instead, a microvesicle sample from the brain tumor patient serum iseasily accessible. In order to analyze nucleic acids in brain tumorcells, it is easier to analyze nucleic acids in serum microvesicles thatare secreted by brain tumor cells. Therefore, in instances where nucleicacids in microvesicles secreted by tissue cells are used to substitutenucleic acids from tissue cells, it is desirable to obtain high qualitynucleic acids which, like those obtained from tissue cells directly,contain detectable quality controls, such as 18S and 28S rRNA. In otherinstances, high quality small RNA is desirable. Nucleic acid extractionsdisclosed herein contain such high quality small RNA together with 18Sand 28S rRNA. Such high quality small RNA is important for the accurateassessment of nucleic acids for various purposes, e.g., the expressionlevel of a particular miRNA.

The invention disclosed here further includes a novel, high-qualityprofile of nucleic acids from microvesicles in a biological sample. Suchprofiles are generated by analyzing nucleic acid extractions thatcontain 18S and 28S rRNA. Such profiles may be obtained with the novelmethods disclosed herein. High quality nucleic acid profiles are highlydesirable for many uses, such as for use as a biomarker for a medicalcondition or therapy selection. It is desirable in that such profilesare consistent between samples. Such consistency can hardly be achievedwithout high quality nuclei acid extractions. In one embodiment of thisinvention, a profile of nucleic acids can be obtained by analyzingnucleic acids in microvesicles that are secreted by those cells oforigin. Such microvesicles can be isolated from an easily accessiblebiological sample, e.g., urine, serum or plasma. Such profiles ofnucleic acids many include small RNAs, messenger RNA, microRNA,non-coding RNAs or a combination thereof In a further embodiment of thisinvention, such profiles of nucleic acids may be combined with otherbiomarkers to more accurately achieve certain results.

The profile of nucleic acids for instance can be a collection of geneticaberrations, which is used herein to refer to the nucleic acid amountsas well as nucleic acid variants within the microvesicles. Specifically,genetic aberrations include, without limitation, over-expression of agene (e.g., oncogenes) or a panel of genes, under-expression of a gene(e.g., tumor suppressor genes such as p53 or RB) or a panel of genes,alternative production of splice variants of a gene or a panel of genes,gene copy number variants (CNV) (e.g. DNA double minutes) (Hahn, 1993),nucleic acid modifications (e.g., methylation, acetylation andphosphorylations), single nucleotide polymorphisms (SNPs), chromosomalrearrangements (e.g., inversions, deletions and duplications), andmutations (insertions, deletions, duplications, missense, nonsense,synonymous or any other nucleotide changes) of a gene or a panel ofgenes, which mutations, in many cases, ultimately affect the activityand function of the gene products, lead to alternative transcriptionalsplice variants and/or changes of gene expression level.

The determination of such genetic aberrations can be performed by avariety of techniques known to the skilled practitioner. For example,expression levels of nucleic acids, alternative splicing variants,chromosome rearrangement and gene copy numbers can be determined bymicroarray analysis (U.S. Pat. Nos. 6,913,879, 7,364,848, 7,378,245,6,893,837 and 6,004,755) and quantitative PCR. Particularly, copy numberchanges may be detected with the Illumina Infinium II whole genomegenotyping assay or Agilent Human Genome CGH Microarray (Steemers etal., 2006). Nucleic acid modifications can be assayed by methodsdescribed in, e.g., U.S. Pat. No. 7,186,512 and patent publicationWO/2003/023065. Particularly, methylation profiles may be determined byIllumina DNA Methylation OMA003 Cancer Panel. SNPs and mutations can bedetected by hybridization with allele-specific probes, enzymaticmutation detection, chemical cleavage of mismatched heteroduplex (Cottonet al., 1988), ribonuclease cleavage of mismatched bases (Myers et al.,1985), mass spectrometry (U.S. Pat. Nos. 6,994,960, 7,074,563, and7,198,893), nucleic acid sequencing, single strand conformationpolymorphism (SSCP) (Orita et al., 1989), denaturing gradient gelelectrophoresis (DGGE)(Fischer and Lerman, 1979a; Fischer and Lerman,1979b), temperature gradient gel electrophoresis (TGGE) (Fischer andLerman, 1979a; Fischer and Lerman, 1979b), restriction fragment lengthpolymorphisms (RFLP) (Kan and Dozy, 1978a; Kan and Dozy, 1978b),oligonucleotide ligation assay (OLA), allele-specific PCR (ASPCR) (U.S.Pat. No. 5,639,611), ligation chain reaction (LCR) and its variants(Abravaya et al., 1995; Landegren et al., 1988; Nakazawa et al., 1994),flow-cytometric heteroduplex analysis (WO/2006/113590) andcombinations/modifications thereof Notably, gene expression levels maybe determined by the serial analysis of gene expression (SAGE) technique(Velculescu et al., 1995). In general, the methods for analyzing geneticaberrations are reported in numerous publications, not limited to thosecited herein, and are available to skilled practitioners. Theappropriate method of analysis will depend upon the specific goals ofthe analysis, the condition/history of the patient, and the specificcancer(s), diseases or other medical conditions to be detected,monitored or treated. The forgoing references are incorporated hereinfor their teachings of these methods.

It should be understood that this invention is not limited to theparticular methodologies, protocols and reagents, described herein,which may vary. The terminology used herein is for the purpose ofdescribing particular embodiments only, and is not intended to limit thescope of the present invention, which is defined solely by the claims.

Examples of the presently disclosed subject matter are set forth below.Other features, objects, and advantages of the presently disclosedsubject matter will be apparent from the detailed description, figures,examples and claims. Methods, devices, and materials substantiallysimilar or equivalent to those described herein can be used in thepractice or testing of the presently disclosed subject matter. Exemplarymethods, devices, uses and materials are now described.

Microvesicles in Urine Example 1 Renal Cells Contain MultivesicularBodies

To examine whether renal cells shed microvesicles, we used TransmissionElectron Microscopy (TEM) to determine whether renal cells containmultivesicular bodies that can give rise to microvesicles. Rat kidneywas fixed by intravascular perfusion with 2.0% glutaraldehyde in 0.1 Msodium cacodylate buffer, pH 7.4 (Electron Microscopy Sciences, PA), andkidney slices were further fixed overnight at 4° C. The sample sliceswere rinsed in 0.1 M sodium cacodylate buffer, post-fixed in 1.0% osmiumtetroxide in cacodylate buffer for 1 h at room temperature, rinsed inbuffer again, then rinsed in distilled water (dH₂O) and stained, enbloc, in an aqueous solution of 2.0% uranyl acetate for 1 hour at roomtemperature. The samples were rinsed in distilled water and dehydratedthrough a graded series of ethanol to 100%. The samples were infiltratedwith Epon resin (Ted Pella, CA) by overnight immersion in a 1:1 solutionof Epon:ethanol. The following day samples were placed in fresh Epon forseveral hours and embedded in Epon overnight at 60° C. Thin sectionswere cut on a Reichert Ultracut E ultramicrotome, collected onformvar-coated grids, stained with uranyl acetate and lead citrate.Samples were examined in a JEOL JEM 1011 transmission electronmicroscope at 80 kV. Images were collected using an AMT (AdvancedMicroscopy Techniques, MA) digital imaging system. As shown in FIG. 1,transmission electron microscope (TEM) images of MVBs are seen in ratrenal tissue cells. Multivesicular bodies (MVB) can be identified invarious regions of the nephron and collecting duct, including thepodocyte, the proximal tubule, thin descending limb, thick ascendinglimb, collecting duct principal cell, and collecting duct intercalatedcell. This demonstrates that exosomes can indeed be released fromvarious regions of the nephron as well as both intercalated andprincipal cells of the collecting duct.

Example 2 Microvesicles Exist in Urine

To examine microvesicles themselves, we examined human urinarymicrovesicles by TEM. Human urine was obtained under the approved IRBguidelines of the Massachusetts General Hospital. Urine was thenpre-processed by a method consisting of three steps: centrifugation ofthe urine at 300 g for 10 min at 4° C., centrifugation of thesupernatant at 17,000 g for 20 min at 4° C., and filtration of thesupernatant through a 0.8 [tm filter (cellulose nitrate membrane filterunit, Nalgene, NY). Alternatively, urine was pre-processed by a one-stepfiltration directly through a 0.8 [tm filter without anypre-centrifugation steps. In either case, the filtrate then underwentultracentrifugation at 118,000 g for 70 min at 4° C., the supernatantwas removed and the microvesicle-containing pellet was washed in PBS andre-pelleted at 118,000 g for 70 min at 4° C.

Instead of ultracentrifugation, filtration concentration was also usedto isolate microvesicles from pre-processed samples. The filtrateconcentrator (100 kDa MWCO) (Millipore, Mass.) was prepared according tothe manufacturer's instructions. Pre-processed filtrate was added to thefiltration concentrator and centrifuged at 4,000 g for 4 min at RT. A 15ml PBS wash step was included.

Microvesicle pellets were fixed, 1:1 with 4% paraformaldehyde in dH₂O.Ten (10) pl drops were pipetted onto formvar-coated 200 mesh gold gridsand drawn off after one minute. Samples were rinsed 2 times with dropsof dH₂O. Aqueous 2.0% phosphotungstic acid (PTA) was applied (10 pl) for10 sec, drawn off and rinsed once with dH₂O. Samples were examined in aJEOL JEM 1011 transmission electron microscope at 80 kV. Images werecollected using an AMT (Advanced Microscopy Techniques, MA) digitalimaging system. As shown in FIG. 2, the pellet was indeed rich inmicrovesicles. The microvesicles sometimes aggregate together or remainsingular in the TEM image.

Improved Methods for Nucleic Acid Extraction from a Biological SampleExample 3 Ultracentrifugation is Replaceable with FiltrationConcentrator for Purposes of Microvesicle Isolation

We show here that filtration concentrators can yield viablemicrovesicles for RNA extraction similar to the ultracentrifugationmethod. We pre-processed 75 ml urine by centrifugation at 300 g for 10minutes at 4° C. and 17,000 g for 20 minutes at 4° C., and then filteredthrough a 0.8 μm filter as detailed in Example 2. We then isolatedmicrovesicles via a 100 kDa MWCO filtration concentrator (Millipore,Mass.) and via ultracentrifugation both with RNase digestion,respectively, and with and without DNase digestion to removeextra-microvesicular nucleic acid contamination. As shown in FIGS. 3 and4, the ultracentrifugation method and filtration concentration methodyielded similar RNA concentrations from the 75 ml urine samples withultracentrifugation (FIG. 4) at 410±28 pg/ill, and filtrationconcentrator (FIG. 3) at 381±47 pg/ill (Mean±SD). There is nostatistically significant difference between the two yields. These datademonstrate that the use of filtration concentrators is a reliablemethod for solating urinary microvesicles for RNA analysis.

Example 4 Sample Pre-Processing with Only a 0.8 Um Pre-Filtration Stepis Sufficient for Purpose of Microvesicle Isolation

Further, we found that the low speed centrifugation steps at 300 g and17,000 g could be eliminated because urine pre-processing with just a0.8 ilm pre-filtration step was as effective as methods including thelow speed centrifugation steps. As shown in FIGS. 5 and 6, the nucleicacid profile using a method of low speed centrifugation coupled with 0.8[tm pre-filtration (A) is the same as the profile using a method of only0.8 [tm pre-filtration (B).

Example 5 Nucleic Acid Extraction from Urinary Microvesicles withMethods that Include Removal or Mitigation of Adverse Factors

We used an improved method for nucleic acid extraction frommicrovesicles. In this method, we removed adverse factors for highquality nucleic acid extractions before breaking microvesicularmembranes. As shown in FIG. 7, urine samples 100 were pre-processed byfiltering through a 0.8 [inn filter membrane 110. The microvesicles inthe filtrates were then isolated either by ultracentrifugation or byfiltration concentration 120, with details similar to those described inExample 2. The isolated microvesicles were then subjected to RNaseand/or DNase digestion to remove nucleic acids not contained inside themicrovesicles 130. Specifically, the microvesicles were resuspended in 1[il/ml RNase A (DNase and protease free) (Fermentas, Md.) in PBS andincubated for 1 hr at 37° C. The samples were re-pelleted at 118,000 gfor 70 min in PBS. For DNase I digestion the pellet was resuspended in500 ul PBS and DNase I (RNase free)(Qiagen, CA) diluted in RDD buffer(according to manufacture's instructions) and incubated at roomtemperature for 10 min. The samples were re-pelleted at 118,000 g for 70min in PBS. For RNase A and DNase I digestion of microvesicles isolatedvia filtration concentrators, the same concentration of RNase and DNasewas used and incubations were carried out in the filtrationconcentrators. A step of extraction enhancement 140 was then performed,e.g., three resuspension/wash steps with 15 ml of PBS alone, or coupledwith a protease treatment. After microvesicles were isolated, digestedwith nucleases and treated with protease, nucleic acids were extracted150. The RNA extraction was performed using the RNeasy Micro kit(Qiagen, CA) according to the manufacturer's instructions. Briefly, 350ul RLT buffer (with 10 ul beta-mercaptoethanol per ml RLT) was used tolyse exosomes and 16 ul nuclease-free water was used for elution. TheRNeasy Plus Micro kit (Qiagen, CA) is designed to remove genomic DNA(gDNA) and was carried out according to the manufacturer's instructionsand eluted in 16 ul nuclease-free water. For small RNA isolation usingthe RNeasy Micro kit or RNeasy Plus Micro kit, the miRNA isolationmethod was followed according to the manufacturer's instructions.Isolated RNA was analyzed 160 on a RNA Pico 6000 chip (Agilent, CA)using a Agilent BioAnalyzer (Agilent, CA) which generated anelectrophoretic profile and corresponding ‘pseudo gel’ of the sample.

As shown in FIGS. 8 and 9, the quality (in terms of yield and integrity)of RNA extraction from urine microvesicles increases as more protease isused to treat microvesicles before breaking the membrane ofmicrovesicles. In FIG. 8, nucleic acids from microvesicles in 20 mlurine were extracted using the above improved method except that the RNAextraction was performed using the Qiagen Qiamp minelute virus spin kit.The urine sample was concentrated with filtration concentration andeluted in 200 pl PBS. Here, we define 1× protease as 0.027 AU; 5×protease as 0.135 AU; 10× protease as 0.27 AU; 25× protease as 0.675 AU;and 50× as 1.35 AU. 18S and 28S rRNA peaks of greater integrity wereobserved when the concentration of protease was increased from 5× (A) to10× (B). Likewise, as shown in FIG. 9, at higher concentrations ofprotease, 25× (A) and 50× (B), we observed 18S and 28S rRNA of higherintegrity, in addition to increased small/miRNA levels. These datasuggest that the addition of protease can increase the yield andintegrity of 18S and 28S rRNA as well as small RNA and microRNA. Wesuspect that the effect of protease may be due to its ability to digestaway RNases and other inhibitory factors.

The addition of a step of washing microvesicles multiple times alsodramatically improves the quality of nucleic acids extracted fromurinary microvesicles. The washing step can effectively remove adversefactors that prevent high quality nucleic acid extraction from urinarymicrovesicles. Urine samples of 20 ml each are used for four groups ofnucleic acid extraction tests following the above method with exceptsome modifications. For group 1, isolated microvesicles were directlyused for nucleic acid extraction without any intervening steps. Forgroup 2, microvesicles were treated with RNase inhibitors before nucleicacid extraction. For group 3, microvesicles were washed without anyRNase inhibitor treatment before nucleic acid extraction. For group 4,microvesicles were washed and treated with RNase inhibitors. As shown inFIG. 38, for group 1 tests, the quality of the extracted nucleic aidswas very poor with RIN of 3.63+2.3 and RNA concentration of 101.3+27.6pg/ul. For group 2 tests (FIG. 39), the quality of the extracted nucleicacids was roughly similar to that in group 1 tests with RIN of 1.83+2.2and RNA concentration of 101.6+88 pg/ul. For group 3 tests (FIG. 40),the quality of the extracted nucleic acids was improved dramaticallywith RIN of 9.2+0.0 and RNA concentration of 347.7+97.7 pg/ul. For group4 tests (FIG. 41), the quality of the extracted nucleic acids wassimilar to that in group 3 with RIN of 7.43+0.2 and RNA concentration of346.3+32.7 pg/ul. These data showed that without washing steps, theextraction quality from microvesicles were inconsistent, with arelatively higher variation than those extractions where microvesicleshad been washed before nucleic acid extraction.

Example 6 Use of RNase Inhibitors for Nucleic Acid Extraction from SerumMicrovesicles

With the above improved method, high quality nucleic acid extractionscan also be obtained from serum microvesicles. Here, we obtained serumfrom both melanoma and normal patient sera and used RNase inhibitorcocktail SUPERase-In™ (Ambion, Inc.) to treat microvesicle pellets byresuspension. In one batch of tests, we isolated microvesicles from fourduplicates of 1 ml melanoma serum samples and treated the microvesiclepellets with 1.6 units SUPERase-In/u1 at a final concentration. Themicrovesicle isolation method was ultracentrifugation and themicrovesicle pellets were treated with DNase for 20 minutes at roomtemperature. As shown in FIGS. 10-13, the quality of RNA extraction fromthe four melanoma serum samples was low and inconsistent, with the RNAyield being 543 pg/ul, 607 pg/ul, 1084 pg/ul, 1090 pg/ul, and the RNAintegrity assessed by the 28s/18s ratio being 1.7, 1.8, 1.3, and 0.6,respectively. In another batch of tests, we isolated microvesicles fromtwo duplicates of 1 ml melanoma serum samples and treated themicrovesicle pellets with 3.2 units SUPERase-In [ill at a finalconcentration. As shown in FIGS. 14 and 15, the quality of RNAextraction from the two melanoma serum samples treated with 3.2 unitsSUPERase-In/pl was generally better than the quality of RNA extractionfrom those treated with 1.6 units SUPERase-In/[d. The RNA yield for thetwo melanoma serum samples is 3433 pg/iAl and 781 pg/pl and the 28S/18Sratio is 1.4 and 1.5, respectively.

Further, we tested four duplicates of 1 ml normal serum samples at 1.6units SUPERase-In/pl and 2 duplicates of 1 ml normal serum samples at3.2 SUPERase-In/[d. As shown in FIGS. 16-19, the quality of RNAextraction at 1.6 units SUPERase-In4 tl is low with the RNA yield being995 pg/pl, 1257 pg/pl, 1027 pg/pl, and 1206 pg/pl, and the 28S/18S ratiobeing 1.3, 1.6, 1.6, 1.8, respectively. In contrast, as shown in FIGS.20 and 21, the quality of RNA extraction at 3.2 units SUPERase-In/ulincreases with the RNA yield being 579 pg/pl and 952 pg/i.il, and the28S/18S ratio being 1.6 and 2.3, respectively.

Example 7 Use of Extraction Enhancement Agents for Nucleic AcidExtraction from a Biological Sample

In Examples 3 and 4, our test results suggest that treatment withextraction enhancers can increase the quality of RNA extraction frommicrovesicles. It is expected that such extraction enhancers will havesimilar effects on other biological samples. As shown in FIG. 22, anovel method of nucleic acid extraction in this invention will require astep of performing an extraction enhancement operation on the biologicalsample. Such method may be exemplified in the following conceivednucleic acid extraction experiment. A doctor prescribes a test of atumor biomarker for a patient. A 5 ml blood is then drawn from thepatient. The blood sample 200 is sometimes pre-processed to get theblood serum. An enhancement operation 210 is then performed, e.g., anappropriate amount of extraction enhancer is added to the serum and themixture is incubated for 30 minutes at 37° C. Nucleic acids from thetreated serum are then extracted using regular extraction methods suchas detailed in Example 5 220 and analyzed using Agilent BioAnalyzer 230.Such extraction is expected to produce high quality nucleic acids fromthe biological sample.

Nucleic Acids from Urinary Microvesicles as Biomarkers Example 8 UrinaryMicrovesicles are Contaminated by Free, Extra-Microvesicle, Non-CellularDNA

We separated a urine sample into two 25 ml duplicate samples andisolated microvesicles from the two sub-samples by differentialcentrifugation as detailed above. In one sub-sample, we treated themicrovesicles with DNase and extracted nucleic acids from the treatedmicrovesicles as detailed above. In another sub-sample, we did not treatthe microvesicles with DNase and extracted nucleic acids from theuntreated microvesicles. As shown in FIG. 23, free, extra-microvesicle,non-cellular DNA contaminated isolated urinary microvesicles. WhenRNeasy micro kit was used for the nucleic acid extraction (FIGS. 23A andB), the result showed that more nucleic acids were seen in the untreatedsample (A) than the treated sample (B) since the peak in (A) wasgenerally higher than the peak in (B).

In another test, we performed a similar test except that serum sampleswere used instead of urine samples. As shown in FIG. 24, free,extra-microvesicle, non-cellular DNA also contaminated the isolatedserum microvesicles. More nucleic acids were seen in the DNase untreatedsample (A) than the DNase treated sample (B) since the peak in (A) wasgenerally higher than the peak in (B). Similarly, when MirVana kit wasused for the nucleic acid extraction, as shown in FIGS. 23 (C) and (D),the result also showed that more nucleic acids were seen in theuntreated sample (C) than the treated sample (D) since the peak in (C)was generally higher than the peak in (D). The extra nucleic acids fromthe untreated sample were likely from DNase susceptible “apoptoticbodies” because DNase susceptible “apoptotic bodies”-like ladders wereseen as shown in the pseudo gel in FIG. 24C. In both the urine and theserum samples, the amount of the free, extra-microvesicle, non-cellularDNA varied between subjects but the size of this DNA was in the range ofapproximately 25 to 1500 base pairs.

Example 9 Urinary Microvesicles are Mostly not Contaminated by Free,Extra-Microvesicle, Non-Cellular RNA

We separated a urine sample into two 25 ml duplicate samples andisolated microvesicles from the two sub-samples by differentialcentrifugation as detailed above. In one sub-sample, we treated themicrovesicles with RNase and extracted nucleic acids from the treatedmicrovesicles as detailed above. In another sub-sample, we did not treatthe microvesicles with RNase and extracted nucleic acids from theuntreated microvesicles. As shown in FIG. 25, almost no free,extra-microvesicle, non-cellular RNA contaminated the isolatedmicrovesicles. The curve of the RNase untreated sample (A) mostlyoverlapped with the curve of the RNase treated sample (B), suggestingthere is no free extra-microvesicle, noncellular RNA associated with theisolated microvesicles. This may be due to the presence of ribonucleasesin urine.

Example 10 Nucleic Acid Profiles are Similar in Urinary Microvesiclesand Renal Cells Measured by Agilent BioAnalyzer

We extracted nucleic acids from both urinary microvesicles and renal(kidney) tissues and compared their profiles. The method of extractionfrom urinary microvesicles was as detailed in Example 5. The rat kidneysamples were processed via the RNeasy Mini kit and the RNeasy Plus kit.To determine the amount of small RNAs in the rat kidney sample, theywere also processed by both kits using the miRNA isolation methodaccording to the manufacturer's instructions.

As shown in FIG. 26, their profiles (A-kidney, B-microvesicle) were verysimilar including the presence and integrity of the 18S and 28S rRNApeaks. Such 18S and 28S rRNA peaks had not been seen in previouslyreported serum-derived or cell culture media-derived microvesicles.

In addition to the similarities in rRNA peaks, urinary microvesiclesalso contained similar small RNA profiles to those obtained from renalcells. As shown in FIG. 27, both urinary microvesicles (B) and renaltissue (A) contained small RNAs (about 25-200 base pairs) and sharedsimilar patterns.

These data suggest that using the novel nucleic acid extraction methoddisclosed in this invention, the profiles in urinary microvesicles maybe used to examine the profiles in the renal cells from which themicrovesicles originated.

Example 11 RNA Profiles in Urinary Microvesicles are Different fromThose from Whole Urine

We discovered that RNA profiles in urinary microvesicles are differentfrom those from whole urine. We used 75 ml duplicate urine samples forthe tests. RNA was isolated from urinary microvesicles by firstpre-processing the urine by 300 g for 10 min at 4° C., centrifugation ofthe supernatant at 17,000 g for 20 min at 4° C., and filtration of thesupernatant through a 0.8 [tm filter (cellulose nitrate membrane filterunit, Nalgene, NY), followed by the steps as detailed in Example 5. RNAfrom whole urine was isolated using the ZR urine RNA isolation kit (ZymoResearch, CA) according to the manufacturer's instructions. To removeDNA from the Zymo processed sample, the eluted RNA was resuspended in350 pl RLT buffer and processed via the RNeasy Plus Micro kit, whichused DNase to eliminate associated DNA, and eluted in 16 pl nucleasefree water.

As shown in FIG. 28, a large amount of nucleic acid could be isolatedusing the ZR urine RNA isolation kit when no DNase was used (A).However, the profile appeared broad and lacked 18S and 28S rRNA peaks.Further, the profile changed significantly (B) when DNase was used,suggesting most of the extract was DNA in nature. In contrast, as shownin FIG. 29, the RNA profile from microvesicles from the same urinesample was generally very different from the profile from the wholeurine extraction. In the microvesicle profile, there were 18 S and 28Speaks. In addition, RNA from microvesicles was more abundant than thatfrom the whole urine. DNase digestion of the extractions frommicrovesicles did not affect the rRNA peak significantly when wecompared the profile without DNase treatment (A) to the profile withDNase treatment (B). The RNA profiles from the 300 g pellets (FIG. 30)and the 17,000 g pellets (FIG. 31) were similar to that from the wholeurine extraction. In both of these profiles, the peaks decreasedsubstantially after DNase treatment when we compared the profile withoutDNase treatment (A) to the profile with DNase treatment (B). These datasuggested that DNA was the predominant species in the extraction, and no18S and 28S rRNA peaks were detectable. Therefore, together with thedata in Example 10, RNA profiles from urinary microvesicles is moresimilar to renal cell profiles than to profiles from whole urine.Further, the integrity of RNA extraction from microvesicles was at least10 times better than that from whole urine.

Example 12 Urinary Microvesicles Contain Both RNA and DNA

We determined whether urinary microvesicles contained RNA, DNA, or bothby treating the pellets first with both RNase and DNase to remove free,extra-microvesicle, non-cellular contaminations followed by RNase and/orDNase digestion of intra-microvesicle nucleic acids during column basednucleic acid isolation. RNase digestion (B) almost completely abolishedthe nucleic acid profile (FIG. 32) compared to that without RNasedigestion (A). These data suggest that RNA represents the most abundantnucleic acid within microvesicles. As shown in FIG. 33, after on-columndigestion of the RNase treated samples with DNase (B), the peak justafter 20s is reduced after further DNase digestion inside in comparisonwith the peak before further DNase digestion (A). This reductiondemonstrated that a small amount of DNase-digestible material waspresent within microvesicles, probably DNA.

Example 13 Urinary Microvesicles Contain mRNA Transcripts EncodingSpecific Genes from Various Regions of the Nephron and Collecting Duct

As shown in Example 10, nucleic acid profiles are similar in urinarymicrovesicles and renal cells measured by Agilent BioAnalyzer. Here wefurther show that microvesicles contain mRNA transcripts encodingspecific genes from various regions of the nephron and collecting duct.Urinary microvesicles were isolated from 200 ml urine from four humansubjects (23 to 32 years of age) and were digested with RNase and DNaseprior to exosome lysis and RNA extraction as detailed in Example 5. Theextracted RNA underwent two rounds of mRNA amplification using RiboAmp(Molecular Devices, CA). For the riboamplification for the first roundof the in vitro transcription step samples were incubated at 42° C. for4 hours and for the second in vitro transcription step samples wereincubated at 42° C. for 6 hours. Amplified RNA was denatured for 5minutes at 65° C. and subjected to first strand cDNA synthesis asdescribed in the Qiagen Omniscript protocol (Qiagen, CA). Both GAPDH andbeta-actin genes were identified in all samples (FIG. 34A). We examined15 transcripts characteristic of various regions of the nephron andcollecting duct (FIG. 34B). These included proteins and receptorsimplicated in various renal diseases including podocin from theglomerulus, cubilin from the proximal tubule and aquaporin 2 from thecollecting duct.

For human samples, the PCR primers used were: ACTB UTR, forward5′-GAAGTCCCTTGCCATCCTAA-3′, reverse ‘5-GCTATCACCTCCCCTGTGTG-3’; GAPDHEX, forward 5′-ACACCCACTCCTCCACCTTT-3′, reverse5′-TGCTGTAGCCAAATTCGTTG-3′; NPHS2 UTR, forward5′-AACTTGGTTCAGATGTCCCTTT-3′, reverse 5′-CAATGATAGGTGCTTGTAGGAAG-3′;LGALS1 EX, forward 5′-GGAAGTGTTGCAGAGGTGTG-3′, reverse5′-TTGATGGCCTCCAGGTTG-3′; HSPG2 UTR, 5′-AAGGCAGGACTCACGACTGA-3′, reverse5′-ATGGCACTTGAGCTGGATCT-3′; CUBN EX, forward 5′-CAGCTCTCCATCCTCTGGAC-3‘, reverse 5’-CCGTGCATAATCAGCATGAA-3′; LRP2 EX, forward5′-CAAAATGGAATCTCTTCAAACG-3′, reverse 5′-GTCGCAGCAACACTTTCCTT-3′; AQP 1UTR, forward 5′-TTACGCAGGTATTTAGAAGCAGAG-3′, reverse5′-AGGGAATGGAGAAGAGAGTGTG-3′; CA4 UTR, forward5′-ATGATGGCTCACTTCTGCAC-3′, reverse 5′-TCATGCCTAAAGTCCCACCT-3′; CLCN5EX, forward 5′-GTGCCTGGTTACACACAACG-3′, reverse5′-AGGATCTTGGTTCGCCATCT-3′; BDKRB1 UTR, forward 5′-GTGGTTGCCTTCCTGGTCT-3‘, reverse 5’-ATGAAGTCCTCCCAAAAGCA-3 ‘; CALCR UTR, forward5’-ATTTTGCCACTGCCTTTCAG-3′, reverse 5′-ATTTTCTCTGGGTGCGCTAA-3′; SCNN1 DUTR, forward 5′-GCGGTGATGTACCCATGCT-3 ‘, reverse5’-CTGAGGTGGCTAGGCTTGA-3 ‘; SLC12A3 EX, forward5’-AGAACAGAGTCAAGTCCCTTCG-3′, reverse 5′-TATGGGCAAAGTGATGACGA-3′; AQP2UTR, forward 5′-GCAGTTCCTGGCATCTCTTG-3′, reverse 5‘-GCCTTTGTCCTTCCCTAACC-3’; ATP6V1B1 EX, forward5′-AGGCAGTAGTTGGGGAGGAG-3′, reverse 5′-CGAGCGGTTCTCGTAGGG-3′; SLC 12A 1EX, forward 5′-CAGATGCAGAACTGGAAGCA-3 ‘, reverse5′-GGAAGGCTCAGGACAATGAG-3’. “UTR” refers to primers designed in the UTRand “EX” refers primers designed across exons. The PCR protocol was 5min at 94° C.; 40 s at 94° C.; 30 s at 55° C.; 1 min at 65° C. for 30cycles; and 68° C. for 4 min. For mouse samples the primers used were:AQP2: forward 5′-GCCACCTCCTTGGGATCTATT-3′, reverse5′-TCATCAAACTTGCCAGTGACAAC-3′; V-ATPase B1 subunit: forward5′-CTGGCACTGACCACGGCTGAG-3′, reverse 5′-CCAGCCTGTGACTGAGCCCTG-3′. ThePCR protocol was 5 min at 94° C.; 40 s at 94° C., 30 s at 55° C., 1 minat 65° C. for 30 cycles; and 68° C. for 4 min.

As shown in FIG. 34, Panel A, RiboAmp amplified mRNA transcripts forbeta-actin and GAPDH were readily detectable in the BioAnalyzergenerated pseudo gel in urinary microvesicles from the four humansubjects. For clarification purpose, the six regions of the nephron andcollecting duct are shown in FIG. 34, Panel B. As a result of RT-PCRanalysis of RiboAmped mRNA from urinary exosomes, the followingtranscripts in the six regions are also readily detectable: region 1Glomerulus: NPHS2—podocin, LGALS1—Galectin-1, and HSPG2—heparan sulfateproteoglycan (FIG. 35); region 2 Proximal Tubule: CUBN—cubilin,LRP2—megalin, AQP1—aquaporin 1, CA4—carbonic anhydrase 4, andCLCNS—chloride channel protein 5 (FIG. 35); region 3 Thin DescendingLimb: BDKRB1—bradykinin B1 receptor (FIG. 36); region 4 Medullary ThickAscending Limb: CALCR—calcitonin receptor, andSCNN1D—amiloride-sensitive sodium channel subunit delta (FIG. 36);region 5 Distal Convoluted Tubule: SLC12A3—thiazide-sensitivesodium-chloride cotransporter (FIG. 36); region 6 Collecting Ducts:AQP2—aquaporin 2, ATP6V1B1—vATPase B1 subunit, andSLC12A1—Kidney-specific Na—K—Cl symporter (FIG. 36).

Therefore, mRNA transcripts from all renal regions examined could beidentified, suggesting that microvesicles containing mRNA are releasedfrom all regions of the nephron and collecting duct, and microvesiclescan be a novel non-invasive source of nucleic acid biomarkers for renaldiseases.

Example 14 Some mRNA Transcripts Inside Urinary Microvesicles areSpecific to Renal Cells

If nucleic acids in microvesicles are used to non-invasively examinerenal genes in diseases, the transcripts in microvesicles should bespecific to renal cells. Here, we show that mRNA transcripts arespecific to renal cells. We used knockout mice in which the V-ATPase B1subunit is absent. The absence of V-ATPase B1 subunit leads to renalacidosis in the mice (Finberg K E, Wagner C A, Bailey M A, et al., TheBI-subunitof the H(+) ATPase is required for maximal urinaryacidification. Proc Natl Acad Sci USA 102:13616-13621, 2005).

All animal experiments were carried out in accordance with approvedanimal ethics guidelines at the Massachusetts General Hospital. V-ATPaseB1 subunit knockout animals have been described (Finberg K E, Wagner CA, Bailey M A, et al. The B1-subunit of the H(+) ATPase is required formaximal urinary acidification. Proc Natl Acad Sci USA 102:1361613621,2005). For urine collection, animals were caged in metabolic cages ingroups of two (n=4 animals per group) over a period of 72 hours(sufficient RNA can also be obtained by caging one animal per cage, andurine was collected for microvesicle isolation and analysis as describedabove for human urine. For kidney extraction, animals were anesthetizedusing pentobarbital sodium (Nembutal) (Abbott Laboratories, IL) (65mg/kg body weight i.p.), and kidneys immediately removed and frozen inliquid nitrogen. Using a pestle and mortar in a liquid nitrogen bath thefrozen kidney was ground up, resuspended in RNAlater (Qiagen, CA) andstored in 1 ml aliquots at −80° C. For RNA extraction, an aliquot wasthawed on ice and 50 pl lysed in 350 pl RLT buffer (with 10 plbeta-mercaptoethanol per ml RLT). Mouse kidney samples were processedvia the RNeasy Mini kit (Qiagen, CA) with the inclusion of the DNAdigestion step.

For real time PCR analysis, RNA extracted from mouse urinarymicrovesicles was denatured for 5 minutes at 65° C. and subjected tofirst strand cDNA synthesis as described in the Qiagen Sensiscriptprotocol (Qiagen, MD). For the Sensiscript reverse transcriptionoligo-dT primers were used at a final concentration of liIM (AppliedBiosystems, CA). The resulting cDNA was used in the TaqMan PreAmp MasterMix Kit according to manufactures guide using 14 preamplification cycles(Applied Biosystems, CA). The preamplification product was then diluted1:20 with 1× TE buffer (Promega, Wis.). The resulting cDNA was then usedas a template for real-time PCR according to Taqman Preamplificationguide (Applied Biosystems, CA). Mouse kidney RNA concentration wasmeasured on a SmartSpec 3000 (Bio-Rad, CA) and all samples were dilutedto 90 ng4.1.1. Mouse kidney RNA was denatured for 5 minutes at 65° C.and subjected to first strand cDNA synthesis as described in the QiagenOmniscript protocol (Qiagen, MD). In the Omniscript reversetranscription oligo-dT primers were used at a final concentration ofliIM (Applied Biosystems, CA) and 1 ill of the resulting cDNA was thenused per well in the subsequent real-time PCR reaction. The real-timePCR reaction was carried out using TaqMan Gene Expression Master Mix andExpression Assays (Mouse GAPD Part Number 4352339E and mouse Atp6vlb2assay id Mm00431996 mH) on an ABI 7300 Real Time PCR System (AppliedBiosystems, CA).

We extracted RNA from kidney tissues as well as from urinarymicrovesicles from the knockout mice. We examined the expression of theV-ATPase B1 subunit and aquaporin 2 (AQP2) mRNA using RT-PCR. As shownFIG. 37, Panel A, V-ATPase B1 subunit transcript was not detected inboth the kidney and urinary microvesicle samples from double mutant mice(B1−/−), which is consistent with the fact that V-ATPase B1 subunit genewas knocked out in these mice. In contrast, V-ATPase B1 subunittranscript was present in the kidney and microvesicle samples from thewild-type mice (B1/+/+). AQP2 mRNA was readily detected in both thekidney and the microvesicle sample from mice with both the B1 knockoutor wild-type mice, which is expected because the V-ATPase B1 subunitdeletion does not affect the expression of AQP2. Further, as shown inFIG. 37, Panel B, the expression level of V-ATPase B2 subunit inmicrovesicles from the B1 knockout was not statistically different fromthe level in microvesicles from the wild-type mice. Such was also truefor the expression level of V-ATPase B2 subunit in kidney cell from theknockout mice in comparison with the level in kidney cells from thewild-type mice. Therefore, transcripts present in kidney cells can bedetected in urinary microvesicles secreted by the kidney cells, andtranscripts absent in kidney cells can not be detected in urinarymicrovesicles secreted by the kidney cell. Accordingly, transcripts inurinary microvesicles are specific to renal cells and are noninvasivebiomarkers for renal cells transcripts.

Example 15 Urinary Microvesicles Contain Non-Coding RNA Transcripts

Urinary microvesicles were isolated and nucleic acids were extractedaccording to the above method detailed in Example 5. We performed adeep-sequencing of urinary microvesicle RNAs and found that there wererandom areas on certain chromosomes that exhibited extremetranscription. When plotted transcript number versus position on thechromosome, these transcripts appeared as “Spikes.” These transcriptswere more abundantly expressed than well-know endogenous markers such asGAPDH or actin, and were generally in non-coding regions of thechromosome. The relatively high expression levels of these spikesequences suggest that these sequences may also serve important roles inchromosome activation and cellular regulation.

We identified 29 regions where there were more than 500 spikes. The 29regions are shown in FIG. 42 and correspond to SEQ ID NOS. 1-29. Theplotted spikes in these 29 regions are shown in FIGS. 45-73. PCRanalysis of the sequences of the most highly expressed spike transcriptsdemonstrated that they were indeed present within both human urinarymicrovesicles and human kidney cells, suggesting that these sequenceswere not an artifact of deep sequencing. The primers used to amply the10 such spike abundant regions are shown in FIG. 43. PCR was performedaccording to the following program: initial denaturing at 95° C. for 8minutes; 30 cycles of three steps of denaturing at 95° C. for 40seconds, annealing at 55° C. for 30 seconds, and elongation at 65° C.for 1 minute; final elongation at 68° C. for 5 minutes; and on hold at4° C. before BioAnalyzer analysis of the reaction. As shown in FIG. 44,the amplification of each of these 10 regions gave positive resultsusing templates in both human urinary microvesicles (A) and human kidneycells (B), suggesting that these spike transcripts were indeed presentwithin microvesicles and human kidney cells.

These abundant spike transcripts can be used to assess the quality of annucleic acid extraction from a biological sample. For example, theamount of any of the spike transcripts can be used to assess the qualityof nucleic acids from urinary microvesicles in place of common markerssuch as GAPDH or ACTIN polynucleotide molecules. The amount of GAPDH orACTIN RNA in urinary microvesicles was so low that anextra-amplification step, e.g., a RiboAMP, was required for measuringtheir amount. In contrast, the amount of any one of the spiketranscripts was so high that no extra-amplification step was necessary.Therefore, the use of these spike transcripts can make the assessment ofnucleic acid extraction quality more efficient and simpler. Hence,another aspect of the inventions described herein is a novel method ofassessing the quality of a nucleic acid extraction from a biologicalsample, e.g., a human urine sample. The method can be accomplished byextracting nucleic acids from a biological sample, measuring the amountof any of the spike transcripts, and compare the amount to a standardthat has been establish for the particular biological sample. Theestablishment of such standard can be, for example, an average amount ofsuch spike transcript extracted from 10 normal human urine samplesperformed by an experienced biotechnology professional.

While the present invention has been disclosed with reference to certainembodiments, numerous modifications, alterations, and changes to thedescribed embodiments are possible without departing from the sphere andscope of the present invention, as defined in the appended claims.Accordingly, it is intended that the present invention not be limited tothe described embodiments, but that it has the full scope defined by thelanguage of the following claims, and equivalents thereof.

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What is claimed is:
 1. A method of evaluating the yield, integrity oryield and integrity of a nucleic acid extraction prepared frommicrovesicles isolated from a biological sample, prior to furtheranalysis of one or more specific nucleic acids in the nucleic acidextraction, the method comprising: (a) obtaining a biological samplecontaining microvesicles from a subject; (b) subjecting the biologicalsample to: i) low speed centrifugation to concentrate proteins, lipids,debris from dead cells, and other contaminants into a pellet fraction,to thereby generate a pre-processed supernatant containingmicrovesicles; ii) filtration to remove proteins, lipids, debris fromdead cells, and other contaminants, to thereby generate a pre-processedfiltrate containing microvesicles; or iii) low speed centrifugation toconcentrate proteins, lipids, debris from dead cells, and othercontaminants into a pellet fraction, to thereby generate a supernatantcontaining microvesicles, followed by filtration of the supernatant toremove proteins, lipids, debris from dead cells, and other contaminants,to thereby generate a pre-processed filtrate containing microvesicles;(c) Subjecting the pre-processed supernatant or pre-processed filtrategenerated in step (b) to i) ultracentrifugation to thereby concentratethe microvesicles into a pellet fraction; or ii) filtrationconcentration to thereby concentrate the microvesicles into a pelletfraction; (d) washing the pellet fraction generated in step (c) tothereby produce a processed microvesicle fraction; (e) extractingnucleic acid from the processed microvesicle fraction generated in step(d) to thereby produce a nucleic acid extraction; (f) measuring theyield, integrity or yield and integrity of the nucleic acid extractionby detecting the presence and quantity of 18S and 28S rRNA in thenucleic acid extraction; (g) evaluating the nucleic acid extraction ashigh yield, high integrity or high yield and high integrity when 18S and28S rRNA is detected in the nucleic acid extraction, with increasedquantity of the 18S and 28S rRNA indicating increased yield andintegrity of the nucleic acid extraction; and (h) further analyzing oneor more specific nucleic acids from a nucleic acid extraction evaluatedas a high yield, high integrity or high yield and high integrity by step(g).
 2. The method of claim 2, wherein the biological sample is a bodilyfluid.
 3. The method of claim 3, wherein the bodily fluid is urine. 4.The method of claim 3, wherein the bodily fluid is serum or plasma. 5.The method of any one of claim 1, wherein the biological sample is froma mammal.
 6. The method of claim 27, wherein the biological sample isfrom a human.
 7. The method of any one of claim 1 further comprisingdetermining a quantitative ratio of 18S rRNA to 28S rRNA in theextraction, wherein the quantitative ratio of 18S rRNA to 28S rRNA iswithin the range of 1:1 to 1:2; and is preferably 1:2.
 8. The method ofclaim 7, wherein the biological sample is urine with a proteinconcentration of less than 10 mg/ml, and the nucleic acid extraction hasan RNA Integrity Number of greater than or equal to
 5. 9. The method ofclaim 7, wherein the biological sample is serum or plasma with a proteinconcentration of greater than 10 mg/ml, and the nucleic acid extractionhas an RNA Integrity Number of greater than or equal to
 3. 10. Themethod of claim 8, wherein 20 ml of biological sample produces a nucleicacid yield greater than or equal to 50 pg/ml.
 11. The method of claim 9,wherein 1 ml of biological sample produces a nucleic acid yield greaterthan or equal to 50 pg/ml.
 12. The method of claim 1, wherein step (e)further comprises detecting an amount of a polynucleotide moleculeselected from SEQ ID NO: 1-29 in the extraction of nucleic acidsobtained from the microvesicle fraction, and comparing the detectedamount to an appropriate standard to assess the yield, integrity oryield and integrity of the nucleic acid extraction.
 13. The method ofclaim 12, wherein the standard is derived by measuring the amount of apolynucleotide molecule comprising a nucleotide sequence selected fromSEQ ID NOS: 1-29 in nucleic acid extractions from more than 5 biologicalsamples.
 14. The method of claim 1, wherein step e) further comprisestreating the processed microvesicle fraction with an RNase inhibitor.15. The method of claim 14, wherein the RNase inhibitor has aconcentration of greater than 1× concentration; alternatively, greaterthan or equal to 5× concentration; alternatively, greater than or equalto 10× concentration; alternatively, greater than or equal to 25×concentration; and alternatively, greater than or equal to 50×concentration.
 16. The method of any claim 14, wherein the RNaseinhibitor is a protease.
 17. The method of claim 1, wherein filtrationstep (b) is performed with a filter having a pore size of less than orequal to. 0.8 μm.
 18. The method of claim 1, wherein step (b) compriseslow speed centrifugation followed by filtration.
 19. The method of claim18, wherein the low speed centrifugation comprises a firstcentrifugation step at 300 g and a second centrifugation step at 17,000g followed by filtration performed with a 0.8 μm filter.
 20. The methodof claim 1, wherein step (a) further comprises performing an extractionenhancement operation on the biological sample.
 21. The method of claim1, wherein step (c) further comprises performing an additionalextraction enhancement operation on the microvesicles.
 22. The method ofclaim 20, wherein the extraction enhancement operation is comprised of:(a) the addition of one or more of the following agents to themicrovesicles: (i) RNase inhibitor; (ii) protease; (iii) reducing agent;(iv) decoy substrate; (v) soluble receptor; (vi) small interfering RNA,(vii) RNA binding molecule; (ix) RNase denaturing substance; or (b) theperformance of one or more of the following steps prior to nucleic acidextraction: (x) size-separating RNase from the sample; (xii) effectingRNase denaturation through a physical change; or (c) any combination ofthe foregoing addition of agents or steps.
 23. The method of claim 1,wherein the biological sample or microvesicles are treated with aribonuclease, deoxyribonuclease, or a combination thereof, prior to thenucleic acid extraction in step (e).
 24. The method of claim 23, whereinthe step (c) further comprises treating the microvesicles with DNase toeliminate any DNA located outside of or on the surface of themicrovesicles, prior to extracting step e).
 25. The method of claim 22,wherein the decoy substrate comprises synthetic RNA.
 26. The method ofclaim 22, wherein the RNA binding molecule comprises an anti-RNAantibody, a chaperone protein, or an RNase inhibitory protein.
 27. Themethod of claim 22, wherein the RNase denaturing substance comprises ahigh osmolarity solution or a detergent.
 28. The method of claim 22,wherein the RNase denaturation is effecting through a physical changeselected from decreasing temperature and freeze/thaw cycle.
 29. A kitfor obtaining nucleic acids from microvesicles, comprising in one ormore containers: (a) a nucleic acid extraction enhancement agent; (b)DNase, RNase, or both; and